¹Department of Biological Sciences, Biochemistry Building, Imperial College London, London SW7 2AY, UK

Correspondence: Dr MPH Stumpf, Department of Biological Sciences, Biochemistry Building, Imperial College London, London SW7 2AZ, UK. Tel: +44 20 7594 5114; Fax: +44 20 7594 5789; E-mail: m.stumpf@imperial.ac.uk

Revised 12 December 2003; Accepted 21 January 2004; Published online 17 March 2004.

Abstract

Haplotype diversity is controlled by a variety of processes, including mutation, recombination, marker ascertainment and demography. Understanding the extent to which genetic variation at physically linked loci is co-inherited is crucial for the design of the HapMap project and the correct interpretation of the resulting data. In the absence of an analytical theory extensive coalescent simulations are used to disentangle the influence of all of these factors on haplotype diversity. In addition to these qualitative insights, this study also demonstrates (i) that marker spacing and frequency profoundly influence observed levels of haplotype diversity; (ii) that the spectrum of haplotypes contains information about how exhaustively genetic variation in a region is described by a given marker set; and (iii) that so-called haplotype blocks can be generated due by the stochasticity inherent in the recombination process without having to assume variation in the recombination rate.